Monday, February 8, 2010

More Doubts About Primordial Soup

You were probably taught in high school biology class that life arose from a primordial soup--the twentieth century's rendition of Darwin's "warm little pond." Most textbooks show pictorial-type drawings of the early earth as a dynamic environment, full of activity. Sunlight is beaming through the clouds with its all important energy-bearing ultra violet rays; rain is pouring down as lightning strikes bring more needed energy to the surface; volcanic activity creates hot spots with yet more energy and a few stray comets might be seen bringing their organic chemicals to seed the life-giving processes. The evolution machine is revving up its engines. Another figure might have illustrated an experimental arrangement mimicking those early-earth conditions. A primordial soup of various organic compounds brewed as sparks were set off in a gaseous mixture above steaming water. There's only one problem: it doesn't work.

Charles Darwin had speculated that life may have begun in a warm little pond with protein compounds ready to undergo more complex changes. Strangely enough, a century later experiments were found to confirm this vision. It appeared that Darwin just happened to be right and the headlines proclaimed that scientists had created "Life in a test tube."

But a plethora of problems were ignored in the process which textbooks eventually had to acknowledge. The 2004 version of George Johnson's high school text, published by Holt, Rinehart and Winston, for instance, includes the primordial soup section but adds a caveat.

In its Principles of Evolution unit, the student reads the usual narrative of organic molecules forming spontaneously in chemical reactions activated by energy from solar radiation, volcanic eruptions, and lightning. The text recounts the success of primordial soup experiments in synthesizing certain organic compounds and concludes:

These results support the hypothesis that some basic chemicals of life could have formed spontaneously under conditions like those in the experiment.

But this traditional life-in-a-test-tube narrative is then followed by an awkward caveat. As the next section explains,

Recent discoveries have caused scientists to reevaluate [the experiment]. We now know that the mixture of gases used in [the experiment] could not have existed on early Earth. ... Some scientists argue that the chemicals were produced within ocean bubbles. Others say that the chemicals arose in deep sea vents. The correct answer has not been determined yet.

That's a refreshing admission. Now a new evolution paper goes further. As one author put it, commenting on the paper:

Despite bioenergetic and thermodynamic failings, the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup has no capacity for producing the energy vital for life.

"It is time to cast off the shackles of fermentation in some primordial soup," commented another author.

These evolutionists believe deep sea vents are the answer. The vents provide chemical gradients that early life would have used before learning how to create their own gradients. Of course we have no idea, beyond speculation, how this actually could have happened. The cell's energy transfer process (referred to as chemiosmosis), using nutrients to synthesize its own chemical energy (ATP), is astonishingly complex. But no matter, it must have happened:

Far from being too complex to have powered early life, it is nearly impossible to see how life could have begun without chemiosmosis ...

The eighteenth century philosopher and evolutionary thinker David Hume argued that the problem of evil trumped the problem of complexity. Nature may be complex, but it must have evolved because god would not have created this wretched world. Now, two centuries later, complexity is simply dismissed because evolution must have occurred.

27 comments:

There is quite a bit of confusion about the "primordial soup." Some doubt has been thrown on Metabolism First, but evidence has been growing for RNA World at some point in the process.

As for amino acid synthesis, it turns out that they form under widely varying natural conditions. Concerning thermal vents, well, that's a primordial soup of a sort.

Overall, we have the evidence that complex life evolved from more primitive organisms, and that these primitive organisms began shortly after the Earth cooled enough for liquid water to form. But this is very ancient history, and left scant evidence. There's no complete theory of abiogenesis, if that makes you feel any better.

//I have no problem whatsoever admitting that the origin of life hypothesis dealing with "soups" is weak, at best. That, in no way whatsoever, impacts any part of the theory of evolution.//

But of course not, we are only dealing with sub-hypothesis of evolution here(as only these are testable within the framework of metaphysical naturalism),it doesn't matter if all of these were false, we would just continue to search for the answer elsewhere.

The defining element of Evolution is the axiom that life in it's complexity and diversity is the result of material processes in one way or another, with or without common descent, with natural selection as the primary driving force or as a secondary complimentary driving force.

There is a positive aspect to this story: now even the darwinian scientists recognize that the clasic "primordial soup" story is a myth - with no scientific foundation.

Just waiting now for a Thaxton to systematically dismantle the new variety of primordial soup with logical, clear arguments. I guess a lot of the classicalarguments against primordial soup origin of life myth stand euqlly well for the new variation of the fairy tale.

It is laughable to see how much energy and effort the army of faithful darwinists/evolutionsts are scrambling to find something remotely resembling a defensible scientific explanation for their (new variation) "primordial soup" creation myth. Wake up. Step back and think honestly. There is absolute no way energy, random chemical and physical processes can generate the engineering marvel of the simplest life form.

Could you detail for me what that would be? Your creationist bias expects a fully-formed E. coli to pop out of nothingness via a miracle. What is the laugh-ability of a self-catalytic RNA, a simple gradient, catalytic peptides, self-assembling membranes?

The discovery of mimiviruses and other large ancient viruses suggest there may be very deep roots to some very simple molecular organization.

p.s. The OP should not confuse criticism of the Miller-Urey experiment as a total failure of all abiogenesis proposals. He should also not confuse abiogenesis and evolution.

A universe of hot vents and primordial ooze would not help evolutionists

Signature in the Cell - Book Review - Ken PetersonExcerpt: the “simplest extant cell, Mycoplasma genitalium — a tiny bacterium that inhabits the human urinary tract — requires ‘only’ 482 proteins to perform its necessary functions…(562,000 bases of DNA…to assemble those proteins).” ,,, amino acids have to congregate in a definite specified sequence in order to make something that “works.” First of all they have to form a “peptide” bond and this seems to only happen about half the time in experiments. Thus, the probability of building a chain of 150 amino acids containing only peptide links is about one chance in 10 to the 45th power.In addition, another requirement for living things is that the amino acids must be the “left-handed” version. But in “abiotic amino-acid production” the right- and left-handed versions are equally created. Thus, to have only left-handed, only peptide bonds between amino acids in a chain of 150 would be about one chance in 10 to the 90th. Moreover, in order to create a functioning protein the “amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements.” It turns out that the probability for this is about one in 10 to the 74th. Thus, the probability of one functional protein of 150 amino acids forming by random chance is (1 in) 10 to the 164th. If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell

You are conflating the simplest known MODERN bacterium with the earliest life (or pre-life). The odds of a genome spontaneously organizing are vanishingly thin. But what are the odds of a bio-catalyst arising? Proline itself, di-valine and other short peptides are catalytic. Could you calculate the odds of forming those?

Membranes self-assemble. RNAs catalyze a variety of reactions. Although these proposals only show potential routes, and exact details may never be known, your calculations make Mount Impossible out of a molehill.

This is an excellent reference that you should read before you continue posting similar 'calculations.'Chemical evolution: toward the origin of lifePure Appl. Chem., Vol. 79, No. 12, pp. 2101–2117, 2007doi:10.1351/pac200779122101

Some other refs on short peptide catalysts:http://chemgroups.northwestern.edu/scheidt/PDFs/2004_pdfs/102004_Proline_Bharadwaj.pdf.

Doug Axe has shown only 1 in 10^77 of any of the amino acid sequences would perform a specific function. The rest of the sequences would be totally useless for any specific function. Even a child knows you cannot put any piece of a puzzle anywhere in a puzzle. You must have the required piece in the required place.

Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723

A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial CellsExcerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division." http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385

Clearly Axe's number of 1 in 10^77, for finding a specific type of functional protein within sequence space, carries much more weight of integrity when balanced against Szostak's questionable work for finding just 1 in 10^12 for any functional protein whatsoever.

Chemist explores the membranous origins of the first living cell:Excerpt: Conditions in geothermal springs and similar extreme environments just do not favor membrane formation, which is inhibited or disrupted by acidity, dissolved salts, high temperatures, and calcium, iron, and magnesium ions. Furthermore, mineral surfaces in these clay-lined pools tend to remove phosphates and organic chemicals from the solution. "We have to face up to the biophysical facts of life," Deamer said. "Hot, acidic hydrothermal systems are not conducive to self-assembly processes."http://currents.ucsc.edu/05-06/04-03/deamer.asp

Hey BA^77, what is the weight of integrity? Why do you compare Axe's numbers for proteins over 100 AA in length to a discussion of very small catalytic proteins? Isn't Szostak's approach the more relevant one to the issue being discussed?

Most importantly, they are irrelevant to the point, and reinforce my complaint-taking a modern genome and saying the chances of it arising from random nucleotides totally ignores chemical and biological evolution! I suppose I could say buckyballs (fullerene) are impossible because 60 OR 540 carbon atoms have arranged themselves in a precise manner. Each carbon can form four bonds-is that 4^60? (jk) Every time I blow out a candle, I make a little bit.

His experiment explores modern sequence space of a modern fold, probing it for function. Complex? Yes. No one on this thread is discussing the de novo origination of a modern protein. I'd love a reference to anyone who has ever proposed such.

Think simpler.

Proline, glycine, divaline. All catalysts. Not modern, fast catalysts, but catalysts nontheless. Produced under many conditions.

Other than that, I don't know what any of those references do to answer me. Perhaps you could respond in your own words.

The other reference following Axe's describes an engineered protein. Interesting, but irrelevant.

In the second post:

Link 1 is to a researcher of abiogenesis, who is exploring conditions for membrane formation. He has fascinating alternative pathways to the first cell.

Look at Able's record in pubmed. Publications cited by no one but himself. His writings are incoherent and unhelpful. Sorry, but I won't let you take refuge in those ramblings. Make your point!

For example, his prize:"a winning submission would have to provide empirical falsification of The Cybernetic Cut. This principle states that prescriptive information flows only from formalism to physicality over an infinitely deep ravine across a one-way C S Bridge"

Self replication by natural processes would suffice to falsify the null hypothesis. A rather trivial requirement given the staggering claims made for the all mighty power of evolutionary processes to create the staggering levels of information we find in life. But alas you have no such evidence!!! but your blind faith in a godless world shall not be detered by my mere words and I will not try.

I've been through this all before, If you care to, you can read my linked to blog, where all this is addressed:

Doug Axe humorously dismantled one of the latest ploys by materialists to oversell their meager evidence for a "self-replicating RNA molecule" in this following article:

Biologic Institute Announces First Self-Replicating Motor Vehicle - Doug Axe - Excerpt: "So, advertising this as “self-replication” is a bit like advertising something as “free” when the actual deal is 1 free for every 1,600 purchased. It’s even worse, though, because you need lots of the pre-made precursors in cozy proximity to a finished RNA in order to kick the process off. That makes the real deal more like n free for every 1,600 n purchased, with the caveats that n must be a very large number and that full payment must be made in advance." http://biologicinstitute.org/2009/04/01/biologic-institute-announces-first-self-replicating-motor-vehicle/

Stephen Meyer points out that intelligence design was clearly required for even this meager result:

Biological Information: The Puzzle of Life that Darwinism Hasn’t Solved - Stephen C. Meyer Thus, as my book Signature in the Cell shows, Joyce’s experiments not only demonstrate that self-replication itself depends upon information-rich molecules, but they also confirm that intelligent design is the only known means by which information arises. http://www.evolutionnews.org//2009/06/biological_information_the_puz.html

Stephen Meyer Responds to Fletcher in Times Literary Supplement - Jan. 2010 Excerpt: everything we know about RNA catalysts, including those with partial self-copying capacity, shows that the function of these molecules depends upon the precise arrangement of their information-carrying constituents (i.e., their nucleotide bases). Functional RNA catalysts arise only once RNA bases are specifically-arranged into information-rich sequences—that is, function arises after, not before, the information problem has been solved. http://www.evolutionnews.org/2010/01/stephen_meyer_responds_to_flet.html

Axe: It’s even worse, though, because you need lots of the pre-made precursors in cozy proximity to a finished RNA in order to kick the process off.

That's why plant scientists (not botanists silly, but scientists that happen to be plants) don't think animals really reproduce because they need lots of pre-made precursors in cozy proximity to kick the process off. All animals do is acquire their resources from hard working plants and just rearrange them, everything from amino acids and starches to complex vitamins.

Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life - Dec. 2009Abstract: A basic property of life is its capacity to experience Darwinian evolution. The replicator concept is at the core of genetics-first theories of the origin of life, which suggest that self-replicating oligonucleotides or their similar ancestors may have been the first “living” systems and may have led to the evolution of an RNA world. But problems with the nonenzymatic synthesis of biopolymers and the origin of template replication have spurred the alternative metabolism-first scenario, where self-reproducing and evolving proto-metabolic networks are assumed to have predated self-replicating genes. Recent theoretical work shows that “compositional genomes” (i.e., the counts of different molecular species in an assembly) are able to propagate compositional information and can provide a setup on which natural selection acts. Accordingly, if we stick to the notion of replicator as an entity that passes on its structure largely intact in successive replications, those macromolecular aggregates could be dubbed “ensemble replicators” (composomes) and quite different from the more familiar genes and memes. In sharp contrast with template-dependent replication dynamics, we demonstrate here that replication of compositional information is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability (i.e., it cannot substantially depart from the asymptotic steady-state solution already built-in in the dynamical equations). We conclude that this fundamental limitation of ensemble replicators cautions against metabolism-first theories of the origin of life, although ancient metabolic systems could have provided a stable habitat within which polymer replicators later evolved.http://www.pnas.org/content/107/4/1470

In commenting on the precedeing paper Axe states

Explaining Life by Explaining it Away — February 6th, 2010 by Douglas AxeExcerpt: Think of it this way. If no conceivable mixture of small molecules provides even a faint hope for the emergence of metabolism catalyzed by genetically encoded enzymes, then whatever these mixtures may or may not do, they can’t explain life as we see it. And as the evidence now stands, one would be hard pressed to argue that there is even a faint hope.http://biologicinstitute.org/2010/02/06/explaining-life-by-explaining-it-away/

“Pigs don’t fly”Excerpt: One of the most devastating critiques of the new “metabolism first” approaches to the origin of life was leveled two years ago by Leslie Orgel right before he died (Nov. 2007)http://www.creationsafaris.com/crev200801.htm#20080126a

Robert Shapiro just a year earlier had leveled a devastating critique of the alternative genetics-first scenario:

OOL (Origin Of Life) on the Rocks:Excerpt: Robert Shapiro, a senior prize-winning chemist, cancer researcher, emeritus professor and author of books in the field, debunks the Miller experiment, the RNA World and other popular experiments as unrealistic dead ends.http://www.creationsafaris.com/crev200702.htm#20070215a

Again, what is the point? Maybe you should make one, and use references to defend it rather than posting abstracts. You have identified the debate: metabolism first, or genetics first. Interesting that you view the scientific debate driving origin of life research forward as a vindication of anti-abiogenesis beliefs.

The possiblity of a pathway, or more accurately partial speculations, does not amount to proof nor does it have probative value. The fact remains that there is currently no pathway to life or to the first membrane and the continued failure in this regard over the last 60 years does not bode well. It takes faith based on a particular metaphysical view of the world to believe that life can arise in such a manner.

Furthemore, if one presumes a materialist metaphysic, then there really is no such thing as "life" except in so far as one is describe particular patterns of arrangements and rearrangements of molecules. That is, there are only four fundamental forces in this universe and all entities (i.e., particles) act as they do as a result of these forces. The result is that everything is merely patterns of particles acting in accordance with the four fundamental forces. The presence of a telecommunications satellite orbiting earth is just the result of the four forces acting upon the finite number of particles that exist in this universe. Gee, that is persuasive.